The NHS in England has admitted that its new system for funding GP practices may discriminate against poorer patients, as it announced a bailout fund to save surgeries in some of the most deprived parts of the country.

As many as 100 GP surgeries around the country – in deprived inner city areas, remote rural areas, and university practices – have been threatened with closure in recent months, after the Government announced changes to the way GPs are to be funded.

However, in an apparent admission that the plans would disproportionately affect areas with high levels of deprivation, local NHS authorities have offered financial support to surgeries whose patient populations have an index of multiple deprivation score above 35 – a Government measure of poverty rates.

Jeremy Hunt, the Health Secretary, and NHS England are facing an unprecedented High Court challenge over the threat to surgeries, brought by one disabled man in the east of London.

The threat to surgeries has come about because of changes to the complex system of GP funding. Virginia Patania, practice manager at the Jubilee Street Practice in east London, which has led the campaign against closures, said yesterday that the changes had been ill-thought-out and “did not take into any account deprivation and inequalities”.

One formula for funding GPs, known as the Carr-Hill formula, was devised a decade ago. It linked large amounts of money to the number of elderly people on a surgery’s patient list, because evidence suggested that it was older patients who required the most GP care.

However, it was observed at the time that Carr-Hill’s emphasis on the elderly would lead to less funding going to poorer areas where life expectancy is lower.

To plug the gap, a funding stream called the Minimum Practice Income Guarantee (MPIG) was introduced to ensure that surgeries which lost out would still receive their historic levels of income. Surgeries with young patient populations, such as university practices, or those with small patient lists, such as remote rural practices, were also supported by the MPIG.

Last year, the Government announced that it would be scrapping the MPIG, on the basis that it led to uneven funding between different GP surgeries. The Royal College of General Practitioners, the British Medical Association and GPs in deprived, rural and student areas have all warned that these plans could leave their patients without a local GP surgery.

NHS England admitted last year that at least 98 practices were at risk of closure because of MPIG cuts. MPIG funding is currently being phased out over seven years, but for some practices – particularly those in deprived urban areas –the financial impact has been immediate.

However, it has taken until now for concrete financial support to be offered – along with an admission that it is poorer areas that are losing out.

In a letter to GP leaders in London and Surrey & Sussex, NHS England’s London Region said that after meetings with inner-city GPs at risk of closing, it had acknowledged that the plans may be hitting the poor hardest.

“Both in London and in other parts of the country, one of the main themes to arise from these discussions has been whether, in some specific cases, the Carr-Hill formula may not sufficiently reflect relative practice workload because of specific demographic factors, particularly in relation to levels of deprivation,” the letter, sent on Tuesday, states. “Work is currently under way nationally to review the Carr-Hill formula, specifically with a view to giving greater weight to deprivation factors.”

NHS England said Carr-Hill does include a weighting for “deprivation factors”, including funding adjustments for levels of chronic disease and premature mortality – both of which are closely linked to social depravation.

“We announced last year that we were undertaking a review of the formula with a view to giving greater weight to deprivation factors,” a spokesperson said.

The bailout for practices hit by the MPIG withdrawal will only be given to surgeries meeting certain criteria. They must be losing more than £3 per patient in funding due to the changes, no doctor in the practice must earn above £106,100 in pensionable income, they must have a recent record of good quality care, and patient population must have an IMD score above 35.

Frontline view: ‘It's a crying shame’

East London’s Jubilee Street Practice told patients last month it may have to close as early as next year. Many other surgeries in the boroughs of Tower Hamlets and Hackney, two of the most deprived in London are also at risk.

Virginia Patania, practice manager at Jubilee Street, said she was pleased that surgeries hit by the withdrawal of MPIG, Tuesday’s letter from NHS England was “a clear admission of a flaw within the funding formula”.

“There’s an acknowledgement that MPIG was vital for practices that had high deprivation levels so definitely the funding changes did not take into any account deprivation and inequalities,” she told The Independent.

She added that NHS England is taking “the first steps to putting it right, but it is a crying shame that it has taken so much and so long ... because it really was an evident flaw from the start”.

One patient at Jubilee Street, 35-year-old Danny Currie, had launched a lawsuit against Health Secretary Jeremy Hunt and NHS England. He claims that, in bringing in the GP funding reforms, the Government and NHS England had not paid due regard to commitments to reduce inequalities made in the Health and Social Care Act 2012 and NHS Act 2006.